Resistomes of pig and poultry

The resistomes of rural and urban pigs and poultry in Ghana

Tuesday 12 Sep 23


Emilie Egholm Bruun Jensen
Research Assistant
DTU National Food Institute
Presentation from the Research Group for Genomic Epidemiology – 04 September 2023

Limited knowledge of the resistome and bacterial community of livestock in Africa excists. Major changes are happening in livestock production in Ghana, with a transition from traditional small-scale production to large-scale production as well as industrialized production.

In this study, we used a metagenomic approach for quantifying the AMR levels, characterizing the resistomes as well as the gut microbiome of pig and poultry in Ghana.

Fecal samples from 30 pigs, where 16 samples were from a rural production setting and 14 from an urban production setting, and 60 poultry, where 20 were from rural free-range, 20 from urban free-range and 20 from an industrial production setting were DNA extracted and sequenced. The trimmed reads were mapped to the ResFinder and Silva database with KMA.

544 different ARGs were identifyed within the poultry samples, witch tet(W) and tet(Q) being the most abundant, and 688 different ARGs were identified within the pig samples with tet(W) and ant(6)-Ia being the most abundant. The pig and poultry samples differed in their resistome composition, showing clear host-effect with tet(A) being the top driver of pig samples and cat3 and cfc(C) being the top driver of poultry samples.

Industrialized poultry had a higher AMR level per sample compared with rural and urban poultry samples. Interestingly, urban poultry had the lowest AMR level. No difference between the rural and urban pig samples was observed and increased biosecurity (measures taking to prevent introduction and spread of AMR) did not show any significant effect on the AMR levels. However, a larger sample size would benefit this analysis.

The most abundant bacterial genera for both pig and poultry samples were Subdoligranulum. The composition of the gut microbiome showed clear host separation with Streptococcus being the top driver of pig samples and Alistipes being the top driver of poultry samples.

Comparison with pig and poultry samples with 9 European contries (from the EFFORT project) showed Ghanaian poultry having an increased AMR level compared to their European counterparts. The ARG abundance were lower for both urban and rural pigs compared to the European ones. A country effect was observed between Ghana and the rest of the 9 European countries, both in their resistome and bacteriome composition.

With this study we have characterized the gut microbiome and resistome of Ghanaian pig and poultry and shown that indutrialized livestock production is accompanied by an increase of antimicrobial resistance.

Emilie Egholm Bruun Jensen’s presentation

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2 OCTOBER 2023